Capturing multiple IR Codes

Sure, probably the easiest way is to just store the times in a second array. Try something like this:

digitalWrite(B7, 0); // Set B7 to GND
digitalWrite(A8, 1); // Set A8 to 3.3V
// Because we're not using the module, we have to manually pull up the data pin
pinMode(B6,"input_pullup");
// Keep somewhere to put the signal times
var times = [];
var history = [];
// now watch the input
setWatch(function(e) {
  // work out how long the pulse was, in milliseconds
  var pulseLen = 1000 * (e.time - e.lastTime);
  // then save it, if it was less than 1 second
  if (pulseLen < 1000)
    times.push(pulseLen);
  else {
   history.push(new Float32Array(times));
    times = [];
  }
}, B6, {repeat:true});

That'll stick everything in history - it uses Float32Array to make sure it can fit a lot of IR recordings in if you need it.

It's worth checking though - most IR remotes just repeat the same pattern over and over (rather than different ones)